BRI Genomics Data

The vast majority of data handled by the Bioinformatics Core — and by extension, with bripipetools — are generated in the Genomics Core (contact: Vivian Gersuk). Furthermore, most samples that pass through the Genomics Core originate in the BRI Sample Repository (notable exceptions include samples from large grants or studies such as ICAC or ITN).

Protocols

Operations related to experimental processing and data generation of Genomics Core samples are generally described by protocols and are tracked in GenLIMS (see the Databases page). Protocols are classified by type, indicating the overall goal or purpose of a procedure or series of steps. A run represents an identifiable instance of a protocol, typically corresponding to a specific chip, plate, or flow cell. Current protocols and associated run types are listed below.

  • incoming

  • RNA extraction

  • miRNA extraction

  • RNA purification

  • globin reduction

  • cell capture

  • cDNA synthesis

  • library prep

  • custom library prep

  • sequencing

  • qPCR

  • bioinformatics processing [PROPOSED]

Data storage

(isilon, Chaussabel lab share)

Isilon

In 2019, BRI set up the primary storage server for genomics (and other data) to be isilon.brivmrc.org to replace sea-zed-01.brivmrc.org.

Genomics/Bioinformatics shares

NB - Following the implementation of isilon at BRI, the primary data from the sequencing machine (.bcl image files) were separated from the processed data (.fastq sequences and further downstream files) in order to aid in improving disaster recovery efforts by IT. The former (raw data) are stored in the /genomics/ share on Isilon, and should not need to be accessed during normal operations. The processed data (sequencing and otherwise) are stored in the /bioinformatics share region of Isilon. A variety of other data files and code related to processing are also stored under the /bioinformatics/ share, but data are nominally stored in one of several subfolders according to source. These are described as “landing points” below.

Basic landing points

  • Illumina (/mnt/bioinformatics/pipeline/Illumina/)

  • Annotations (``/mnt/bioinformatics/pipeline/annotation/)

  • SRA (/mnt/bioinformatics/workspace/SRA/)

  • ICAC (/mnt/bioinformatics/workspace/ICAC/)

  • NGXBio (/mnt/bioinformatics/workspace/NGXBio/)

  • Fluidigm (/mnt/bioinformatics/workspace/Fluidigm/)

Reference data

/mnt/bioinformatics/workspace/reference_data/

  • annotationsForGalaxy

  • Genomes

  • iGenomes

  • ERCC92

Special folders

  • code (/mnt/bioinformatics/workspace/code/)

  • galaxy_workflows (/mnt/bioinformatics/pipeline/galaxy_workflows/)

  • geo_submissions (/mnt/bioinformatics/workspace/geo_submissions/)

Old Galaxy data

  • /mnt/bioinformatics/pipeline/Archive

Project tracking database

GCQ (Genomics Core Queue) <https://gcq.benaroyaresearch.org/>_

Chaussabel lab share

  • Main lab share: srvstor01/DFS_Chaussabel_LabShare

  • Flowcell log: srvstor01/DFS_Chaussabel_LabShare/Illumina HiScan SQ/Flowcell log.xlsx